I'm not who you asked, but the first thing that comes to my mind is contrib.auth.views, which look for templates at the default locations or the locations you provide (as described here: https://docs.djangoproject.com/en/1.11/topics/auth/default/#... )
So using non-django templates would rule out this kind of thing right?
We've been using Jinja2 at my startup since the beginning; in the four years I'be been working here I can't recall any issues with plug-ins using it.